Re: [gmx-users] Desired density - genbox
On 3/19/13 5:52 AM, Steven Neumann wrote: Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest? If the force field has been parametrized to reproduce the density, then yes. -Justin On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul wrote: On 3/18/13 6:14 PM, Steven Neumann wrote: On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? I think you missed the point of what I was saying. You can use a larger box, with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure coupling to guarantee the box stays cubic). Provided the force field model produces the density you want, that's all you need to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest? Steven On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul wrote: > > > On 3/18/13 6:14 PM, Steven Neumann wrote: >> >> On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote: >>> >>> >>> >>> On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. >>> >>> Use a larger box and equilibrate. >> >> >> Thanks. >> Larger box will need more molecules which is quite obvious so the same >> problem occurs. I need a cubic box first with given fixed density and >> then equilibrate it. Further step is to extend the box in one >> dimension to get properties I want. >> Shall manually add them then? >> > > I think you missed the point of what I was saying. You can use a larger > box, with 850 molecules inserted, and equilbrate under NPT (using isotropic > pressure coupling to guarantee the box stays cubic). Provided the force > field model produces the density you want, that's all you need to do. > > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
On 3/18/13 6:14 PM, Steven Neumann wrote: On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? I think you missed the point of what I was saying. You can use a larger box, with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure coupling to guarantee the box stays cubic). Provided the force field model produces the density you want, that's all you need to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote: > > > On 3/18/13 2:56 PM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am trying to obtain given density for my system for a given molecule >> - its a cubic box of 5 nm in dimension. >> >> I calculated that I need 850 molecules to get the density of 500 g/mol >> In my box there is already 1 molecule so I try: >> >> genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb >> >> >> >> Added 819 molecules (out of 849 requested) >> Output configuration contains 9020 atoms in 820 residues >> Volume : 125 (nm^3) >> Density: 480.336 (g/l) >> Number of SOL molecules: 0 >> >> How can I add 30 more molecules using gromacs? I want to avoid adding >> it manually. >> > > Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? Steven All genbox tries to do is add molecules > randomly, which is not a foolproof process. If the force field parameters > indeed produce the correct density, you should be able to produce it rather > quickly. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. All genbox tries to do is add molecules randomly, which is not a foolproof process. If the force field parameters indeed produce the correct density, you should be able to produce it rather quickly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
